EHV-1 TES dynamics
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TES dynamics
Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.6)... Done.## Bootstrap (r = 0.68)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3535277 0.7032744 0.6285041
## 16: 2 ORF3 0.3535277 0.7032744 0.6285041
## 17: 2 ORF8 0.3535277 0.7032744 0.6285041
## 18: 2 ORF9 0.3535277 0.7032744 0.6285041
## 19: 2 ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 20: 2 ORF18 0.3535277 0.7032744 0.6285041
## 21: 2 ORF22 0.3535277 0.7032744 0.6285041
## 22: 2 ORF23 0.3535277 0.7032744 0.6285041
## 23: 2 ORF24 0.3535277 0.7032744 0.6285041
## 24: 2 ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 25: 2 ORF28, ORF29 0.3535277 0.7032744 0.6285041
## 26: 2 ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 27: 2 ORF36 0.3535277 0.7032744 0.6285041
## 28: 2 ORF37 0.3535277 0.7032744 0.6285041
## 29: 2 ORF38 0.3535277 0.7032744 0.6285041
## 30: 2 ORF39 0.3535277 0.7032744 0.6285041
## 31: 2 CTO 0.3535277 0.7032744 0.6285041
## 32: 2 ORF40 0.3535277 0.7032744 0.6285041
## 33: 2 ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 34: 2 ORF44 0.3535277 0.7032744 0.6285041
## 35: 2 ORF45, ORF46 0.3535277 0.7032744 0.6285041
## 36: 2 ORF48, ORF49, ORF50, ORF51 0.3535277 0.7032744 0.6285041
## 37: 2 ORF66_1 0.3535277 0.7032744 0.6285041
## 38: 3 ORF4 0.8815211 0.9579628 0.8371409
## 39: 3 ORF69, ORF70 0.8815211 0.9579628 0.8371409
## 40: 4 ORF18, ORF17, ORF16, ORF15 0.9713186 0.9914396 0.9076565
## 41: 4 ORF19 0.9713186 0.9914396 0.9076565
## 42: 4 ORF52 0.9713186 0.9914396 0.9076565
## 43: 4 ORF53, ORF54 0.9713186 0.9914396 0.9076565
## 44: 4 ORF57, ORF58 0.9713186 0.9914396 0.9076565
## 45: 4 ORF62, ORF61, ORF60,ORF59 0.9713186 0.9914396 0.9076565
## 46: 4 ORF71, ORF72, ORF73 0.9713186 0.9914396 0.9076565
## 47: 5 ORF64_1 0.8784079 0.9517522 0.8726087
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 2: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 3: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 4: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 5: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 6: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 7: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 8: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 9: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 10: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 11: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 12: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 13: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 14: 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.00000000
## 15: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 16: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 17: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 18: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 19: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 20: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 21: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 22: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 23: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 24: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 25: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 26: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 27: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 28: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 29: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 30: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 31: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 32: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 33: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 34: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 35: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 36: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 37: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 38: 0.01713282 0.007812127 0.004060461 -1.3551469 0.3723721 0.35827823
## 39: 0.01713282 0.007812127 0.004060461 -1.3551469 0.3723721 0.35827823
## 40: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 41: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 42: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 43: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 44: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 45: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 46: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 47: 0.01816271 0.009126113 0.003661387 -1.4004477 0.2616381 0.81800102
## se.si se.au se.bp v c pchi
## [1] "ORF44" "ORF48, ORF49, ORF50, ORF51"
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"## [1] 4## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF9"
## [5] "ORF12, ORF13, ORF14" "ORF18"
## [7] "ORF22" "ORF23"
## [9] "ORF24" "ORF27, ORF26, ORF25"
## [11] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36" "ORF37"
## [15] "ORF38" "ORF39"
## [17] "CTO" "ORF40"
## [19] "ORF41, ORF42, OF43" "ORF44"
## [21] "ORF45, ORF46" "ORF48, ORF49, ORF50, ORF51"
## [23] "ORF66_1"## [1] 23Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3535277 0.7032744 0.6285041
## 16: 2 ORF3 0.3535277 0.7032744 0.6285041
## 17: 2 ORF8 0.3535277 0.7032744 0.6285041
## 18: 2 ORF9 0.3535277 0.7032744 0.6285041
## 19: 2 ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 20: 2 ORF18 0.3535277 0.7032744 0.6285041
## 21: 2 ORF22 0.3535277 0.7032744 0.6285041
## 22: 2 ORF23 0.3535277 0.7032744 0.6285041
## 23: 2 ORF24 0.3535277 0.7032744 0.6285041
## 24: 2 ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 25: 2 ORF28, ORF29 0.3535277 0.7032744 0.6285041
## 26: 2 ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 27: 2 ORF36 0.3535277 0.7032744 0.6285041
## 28: 2 ORF37 0.3535277 0.7032744 0.6285041
## 29: 2 ORF38 0.3535277 0.7032744 0.6285041
## 30: 2 CTO 0.3535277 0.7032744 0.6285041
## 31: 2 ORF40 0.3535277 0.7032744 0.6285041
## 32: 2 ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 33: 2 ORF44 0.3535277 0.7032744 0.6285041
## 34: 2 ORF48, ORF49, ORF50, ORF51 0.3535277 0.7032744 0.6285041
## 35: 2 ORF66_1 0.3535277 0.7032744 0.6285041
## 36: 3 ORF4 0.8815211 0.9579628 0.8371409
## 37: 3 ORF69, ORF70 0.8815211 0.9579628 0.8371409
## 38: 4 ORF18, ORF17, ORF16, ORF15 0.9713186 0.9914396 0.9076565
## 39: 4 ORF19 0.9713186 0.9914396 0.9076565
## 40: 4 ORF52 0.9713186 0.9914396 0.9076565
## 41: 4 ORF53, ORF54 0.9713186 0.9914396 0.9076565
## 42: 4 ORF57, ORF58 0.9713186 0.9914396 0.9076565
## 43: 4 ORF62, ORF61, ORF60,ORF59 0.9713186 0.9914396 0.9076565
## 44: 4 ORF71, ORF72, ORF73 0.9713186 0.9914396 0.9076565
## 45: 5 ORF39 0.8784079 0.9517522 0.8726087
## 46: 5 ORF45, ORF46 0.8784079 0.9517522 0.8726087
## 47: 6 ORF64_1 0.1756737 0.6030497 0.5669824
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 8: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 9: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 10: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 11: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 12: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 13: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 14: 0.00000000 0.000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 15: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 20: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 21: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 22: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 23: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 24: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 25: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 26: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 27: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 28: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 29: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 30: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 31: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 32: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 33: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 34: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 35: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 36: 0.01713282 0.007812127 0.004060461 -1.3551469 0.37237211 0.35827823
## 37: 0.01713282 0.007812127 0.004060461 -1.3551469 0.37237211 0.35827823
## 38: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 39: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 40: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 41: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 42: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 43: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 44: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 45: 0.01816271 0.009126113 0.003661387 -1.4004477 0.26163807 0.81800102
## 46: 0.01816271 0.009126113 0.003661387 -1.4004477 0.26163807 0.81800102
## 47: 0.03647159 0.029011389 0.005231616 -0.2149728 0.04627609 0.45948071
## se.si se.au se.bp v c pchi
## [1] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"## [1] 3## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF9"
## [5] "ORF12, ORF13, ORF14" "ORF18"
## [7] "ORF22" "ORF23"
## [9] "ORF24" "ORF27, ORF26, ORF25"
## [11] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36" "ORF37"
## [15] "ORF38" "CTO"
## [17] "ORF40" "ORF41, ORF42, OF43"
## [19] "ORF44" "ORF48, ORF49, ORF50, ORF51"
## [21] "ORF66_1" "ORF64_1"## [1] 22Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3535277 0.7032744 0.6285041
## 16: 2 ORF8 0.3535277 0.7032744 0.6285041
## 17: 2 ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 18: 2 ORF22 0.3535277 0.7032744 0.6285041
## 19: 2 ORF23 0.3535277 0.7032744 0.6285041
## 20: 2 ORF24 0.3535277 0.7032744 0.6285041
## 21: 2 ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 22: 2 ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 23: 2 ORF36 0.3535277 0.7032744 0.6285041
## 24: 2 CTO 0.3535277 0.7032744 0.6285041
## 25: 2 ORF40 0.3535277 0.7032744 0.6285041
## 26: 2 ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 27: 2 ORF44 0.3535277 0.7032744 0.6285041
## 28: 3 ORF3 0.8815211 0.9579628 0.8371409
## 29: 3 ORF9 0.8815211 0.9579628 0.8371409
## 30: 3 ORF18 0.8815211 0.9579628 0.8371409
## 31: 3 ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 32: 3 ORF37 0.8815211 0.9579628 0.8371409
## 33: 3 ORF38 0.8815211 0.9579628 0.8371409
## 34: 3 ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 35: 3 ORF66_1 0.8815211 0.9579628 0.8371409
## 36: 4 ORF4 0.9713186 0.9914396 0.9076565
## 37: 4 ORF69, ORF70 0.9713186 0.9914396 0.9076565
## 38: 5 ORF18, ORF17, ORF16, ORF15 0.8784079 0.9517522 0.8726087
## 39: 5 ORF19 0.8784079 0.9517522 0.8726087
## 40: 5 ORF52 0.8784079 0.9517522 0.8726087
## 41: 5 ORF53, ORF54 0.8784079 0.9517522 0.8726087
## 42: 5 ORF57, ORF58 0.8784079 0.9517522 0.8726087
## 43: 5 ORF62, ORF61, ORF60,ORF59 0.8784079 0.9517522 0.8726087
## 44: 5 ORF71, ORF72, ORF73 0.8784079 0.9517522 0.8726087
## 45: 6 ORF39 0.1756737 0.6030497 0.5669824
## 46: 6 ORF45, ORF46 0.1756737 0.6030497 0.5669824
## 47: 7 ORF64_1 0.9958011 0.9987219 0.9768648
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 8: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 9: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 15: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 20: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 21: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 22: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 23: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 24: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 25: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 26: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 27: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 28: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 29: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 30: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 31: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 32: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 33: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 34: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 35: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 36: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 37: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 38: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 39: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 40: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 41: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 42: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 43: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 44: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 45: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 46: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 47: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## se.si se.au se.bp v c pchi
## [1] "ORF10, ORF11" "ORF32, ORF33, ORF34" "ORF2"## [1] 3## [1] "ORF2" "ORF8"
## [3] "ORF12, ORF13, ORF14" "ORF22"
## [5] "ORF23" "ORF24"
## [7] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [9] "ORF36" "CTO"
## [11] "ORF40" "ORF41, ORF42, OF43"
## [13] "ORF44" "ORF39"
## [15] "ORF45, ORF46"## [1] 15Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3535277 0.7032744 0.6285041
## 8: 2 ORF8 0.3535277 0.7032744 0.6285041
## 9: 2 ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 10: 2 ORF22 0.3535277 0.7032744 0.6285041
## 11: 2 ORF23 0.3535277 0.7032744 0.6285041
## 12: 2 ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 13: 2 ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 14: 2 ORF36 0.3535277 0.7032744 0.6285041
## 15: 2 CTO 0.3535277 0.7032744 0.6285041
## 16: 2 ORF40 0.3535277 0.7032744 0.6285041
## 17: 2 ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 18: 2 ORF44 0.3535277 0.7032744 0.6285041
## 19: 3 ORF3 0.8815211 0.9579628 0.8371409
## 20: 3 ORF9 0.8815211 0.9579628 0.8371409
## 21: 3 ORF18 0.8815211 0.9579628 0.8371409
## 22: 3 ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 23: 3 ORF37 0.8815211 0.9579628 0.8371409
## 24: 3 ORF38 0.8815211 0.9579628 0.8371409
## 25: 3 ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 26: 3 ORF66_1 0.8815211 0.9579628 0.8371409
## 27: 4 ORF4 0.9713186 0.9914396 0.9076565
## 28: 4 ORF69, ORF70 0.9713186 0.9914396 0.9076565
## 29: 5 ORF7, ORF6, ORF5 0.8784079 0.9517522 0.8726087
## 30: 5 ORF30 0.8784079 0.9517522 0.8726087
## 31: 5 ORF63 0.8784079 0.9517522 0.8726087
## 32: 5 ORF65_1 0.8784079 0.9517522 0.8726087
## 33: 6 ORF10, ORF11 0.1756737 0.6030497 0.5669824
## 34: 6 ORF32, ORF33, ORF34 0.1756737 0.6030497 0.5669824
## 35: 6 NOIR_1 0.1756737 0.6030497 0.5669824
## 36: 6 NOIR_2 0.1756737 0.6030497 0.5669824
## 37: 7 ORF18, ORF17, ORF16, ORF15 0.9958011 0.9987219 0.9768648
## 38: 7 ORF19 0.9958011 0.9987219 0.9768648
## 39: 7 ORF52 0.9958011 0.9987219 0.9768648
## 40: 7 ORF53, ORF54 0.9958011 0.9987219 0.9768648
## 41: 7 ORF57, ORF58 0.9958011 0.9987219 0.9768648
## 42: 7 ORF62, ORF61, ORF60,ORF59 0.9958011 0.9987219 0.9768648
## 43: 7 ORF71, ORF72, ORF73 0.9958011 0.9987219 0.9768648
## 44: 8 ORF24 0.7355745 0.9396843 0.5246778
## 45: 9 ORF39 0.9957254 0.9989872 0.9509454
## 46: 9 ORF45, ORF46 0.9957254 0.9989872 0.9509454
## 47: 10 ORF64_1 0.2640694 0.6976944 0.5265909
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 9: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 10: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 11: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 12: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 13: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 14: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 15: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 20: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 21: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 22: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 23: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 24: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 25: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 26: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 27: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 28: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 29: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 30: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 31: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 32: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 33: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 34: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 35: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 36: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 37: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 38: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 39: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 40: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 41: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 42: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 43: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 44: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 45: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 46: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 47: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## se.si se.au se.bp v c pchi
## character(0)## [1] 0## [1] "ORF2" "ORF8"
## [3] "ORF12, ORF13, ORF14" "ORF22"
## [5] "ORF23" "ORF27, ORF26, ORF25"
## [7] "ORF37, ORF36, ORF35, ORF35.5" "ORF36"
## [9] "CTO" "ORF40"
## [11] "ORF41, ORF42, OF43" "ORF44"
## [13] "ORF10, ORF11" "ORF32, ORF33, ORF34"
## [15] "NOIR_1" "NOIR_2"
## [17] "ORF24" "ORF64_1"## [1] 18Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3535277 0.7032744 0.6285041
## 8: 2 ORF40 0.3535277 0.7032744 0.6285041
## 9: 3 ORF3 0.8815211 0.9579628 0.8371409
## 10: 3 ORF9 0.8815211 0.9579628 0.8371409
## 11: 3 ORF18 0.8815211 0.9579628 0.8371409
## 12: 3 ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 13: 3 ORF37 0.8815211 0.9579628 0.8371409
## 14: 3 ORF38 0.8815211 0.9579628 0.8371409
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 16: 3 ORF66_1 0.8815211 0.9579628 0.8371409
## 17: 4 ORF4 0.9713186 0.9914396 0.9076565
## 18: 5 ORF7, ORF6, ORF5 0.8784079 0.9517522 0.8726087
## 19: 5 ORF30 0.8784079 0.9517522 0.8726087
## 20: 5 ORF63 0.8784079 0.9517522 0.8726087
## 21: 5 ORF65_1 0.8784079 0.9517522 0.8726087
## 22: 6 ORF8 0.1756737 0.6030497 0.5669824
## 23: 6 ORF12, ORF13, ORF14 0.1756737 0.6030497 0.5669824
## 24: 6 ORF22 0.1756737 0.6030497 0.5669824
## 25: 6 ORF23 0.1756737 0.6030497 0.5669824
## 26: 6 ORF27, ORF26, ORF25 0.1756737 0.6030497 0.5669824
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.1756737 0.6030497 0.5669824
## 28: 6 ORF36 0.1756737 0.6030497 0.5669824
## 29: 6 CTO 0.1756737 0.6030497 0.5669824
## 30: 6 ORF41, ORF42, OF43 0.1756737 0.6030497 0.5669824
## 31: 6 ORF44 0.1756737 0.6030497 0.5669824
## 32: 7 ORF10, ORF11 0.9958011 0.9987219 0.9768648
## 33: 7 ORF32, ORF33, ORF34 0.9958011 0.9987219 0.9768648
## 34: 7 NOIR_1 0.9958011 0.9987219 0.9768648
## 35: 7 NOIR_2 0.9958011 0.9987219 0.9768648
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.7355745 0.9396843 0.5246778
## 37: 8 ORF19 0.7355745 0.9396843 0.5246778
## 38: 8 ORF52 0.7355745 0.9396843 0.5246778
## 39: 8 ORF53, ORF54 0.7355745 0.9396843 0.5246778
## 40: 8 ORF57, ORF58 0.7355745 0.9396843 0.5246778
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.7355745 0.9396843 0.5246778
## 42: 8 ORF71, ORF72, ORF73 0.7355745 0.9396843 0.5246778
## 43: 9 ORF24 0.9957254 0.9989872 0.9509454
## 44: 10 ORF39 0.2640694 0.6976944 0.5265909
## 45: 10 ORF45, ORF46 0.2640694 0.6976944 0.5265909
## 46: 11 ORF64_1 0.1824227 0.6866721 0.4571851
## 47: 12 ORF69, ORF70 0.1738705 0.6369552 0.5181925
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 9: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 10: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 11: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 12: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 13: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 14: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 15: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 16: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 17: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 18: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 19: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 20: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 21: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 22: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 23: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 24: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 25: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 26: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 27: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 28: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 29: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 30: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 31: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 32: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 33: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 34: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 35: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 36: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 37: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 38: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 39: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 40: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 41: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 42: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 43: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 44: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 45: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 46: 0.041320411 0.0267774857 0.005255464 -0.1894555 0.29698353 0.96722304
## 47: 0.038302215 0.0281628751 0.005273569 -0.1979748 0.15235721 0.82296434
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF2" "ORF40"
## [3] "ORF8" "ORF12, ORF13, ORF14"
## [5] "ORF22" "ORF23"
## [7] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [9] "ORF36" "CTO"
## [11] "ORF41, ORF42, OF43" "ORF44"
## [13] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [15] "ORF52" "ORF53, ORF54"
## [17] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [19] "ORF71, ORF72, ORF73" "ORF39"
## [21] "ORF45, ORF46" "ORF64_1"
## [23] "ORF69, ORF70"## [1] 23Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3535277 0.7032744 0.6285041
## 8: 2 ORF40 0.3535277 0.7032744 0.6285041
## 9: 3 ORF3 0.8815211 0.9579628 0.8371409
## 10: 3 ORF9 0.8815211 0.9579628 0.8371409
## 11: 3 ORF18 0.8815211 0.9579628 0.8371409
## 12: 3 ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 13: 3 ORF37 0.8815211 0.9579628 0.8371409
## 14: 3 ORF38 0.8815211 0.9579628 0.8371409
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 16: 3 ORF66_1 0.8815211 0.9579628 0.8371409
## 17: 4 ORF4 0.9713186 0.9914396 0.9076565
## 18: 5 ORF7, ORF6, ORF5 0.8784079 0.9517522 0.8726087
## 19: 5 ORF30 0.8784079 0.9517522 0.8726087
## 20: 5 ORF63 0.8784079 0.9517522 0.8726087
## 21: 5 ORF65_1 0.8784079 0.9517522 0.8726087
## 22: 6 ORF8 0.1756737 0.6030497 0.5669824
## 23: 6 ORF12, ORF13, ORF14 0.1756737 0.6030497 0.5669824
## 24: 6 ORF22 0.1756737 0.6030497 0.5669824
## 25: 6 ORF23 0.1756737 0.6030497 0.5669824
## 26: 6 ORF27, ORF26, ORF25 0.1756737 0.6030497 0.5669824
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.1756737 0.6030497 0.5669824
## 28: 6 ORF36 0.1756737 0.6030497 0.5669824
## 29: 6 CTO 0.1756737 0.6030497 0.5669824
## 30: 6 ORF41, ORF42, OF43 0.1756737 0.6030497 0.5669824
## 31: 6 ORF44 0.1756737 0.6030497 0.5669824
## 32: 7 ORF10, ORF11 0.9958011 0.9987219 0.9768648
## 33: 7 ORF32, ORF33, ORF34 0.9958011 0.9987219 0.9768648
## 34: 7 NOIR_1 0.9958011 0.9987219 0.9768648
## 35: 7 NOIR_2 0.9958011 0.9987219 0.9768648
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.7355745 0.9396843 0.5246778
## 37: 8 ORF19 0.7355745 0.9396843 0.5246778
## 38: 8 ORF52 0.7355745 0.9396843 0.5246778
## 39: 8 ORF53, ORF54 0.7355745 0.9396843 0.5246778
## 40: 8 ORF57, ORF58 0.7355745 0.9396843 0.5246778
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.7355745 0.9396843 0.5246778
## 42: 8 ORF71, ORF72, ORF73 0.7355745 0.9396843 0.5246778
## 43: 9 ORF24 0.9957254 0.9989872 0.9509454
## 44: 10 ORF39 0.2640694 0.6976944 0.5265909
## 45: 10 ORF45, ORF46 0.2640694 0.6976944 0.5265909
## 46: 11 ORF64_1 0.1824227 0.6866721 0.4571851
## 47: 12 ORF69, ORF70 0.1738705 0.6369552 0.5181925
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 9: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 10: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 11: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 12: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 13: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 14: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 15: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 16: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 17: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 18: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 19: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 20: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 21: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 22: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 23: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 24: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 25: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 26: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 27: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 28: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 29: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 30: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 31: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 32: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 33: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 34: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 35: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 36: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 37: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 38: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 39: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 40: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 41: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 42: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 43: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 44: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 45: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 46: 0.041320411 0.0267774857 0.005255464 -0.1894555 0.29698353 0.96722304
## 47: 0.038302215 0.0281628751 0.005273569 -0.1979748 0.15235721 0.82296434
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF2" "ORF40"
## [3] "ORF8" "ORF12, ORF13, ORF14"
## [5] "ORF22" "ORF23"
## [7] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [9] "ORF36" "CTO"
## [11] "ORF41, ORF42, OF43" "ORF44"
## [13] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [15] "ORF52" "ORF53, ORF54"
## [17] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [19] "ORF71, ORF72, ORF73" "ORF39"
## [21] "ORF45, ORF46" "ORF64_1"
## [23] "ORF69, ORF70"## [1] 23Remove genes from clusters ?
## [1] "ORF2" "ORF40"
## [3] "ORF8" "ORF12, ORF13, ORF14"
## [5] "ORF22" "ORF23"
## [7] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [9] "ORF36" "CTO"
## [11] "ORF41, ORF42, OF43" "ORF44"
## [13] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [15] "ORF52" "ORF53, ORF54"
## [17] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [19] "ORF71, ORF72, ORF73" "ORF39"
## [21] "ORF45, ORF46" "ORF64_1"
## [23] "ORF69, ORF70"## [1] 23## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 10
## 2: 3 8
## 3: 8 7
## 4: 1 6
## 5: 5 4
## 6: 7 4
## 7: 2 2
## 8: 10 2
## 9: 4 1
## 10: 9 1
## 11: 11 1
## 12: 12 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
